X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FContactMatrix.java;h=48b6e6b45b3476fc97548fbd3ad4bf47ada00b9d;hb=e281f3fc527a483dc69787f9a04bf84e50527e9d;hp=f2e207c596605079ab503ff49c08292d3daf5515;hpb=335e6b12c126bcb6825cd3f66422677db7cd91c7;p=jalview.git

diff --git a/src/jalview/datamodel/ContactMatrix.java b/src/jalview/datamodel/ContactMatrix.java
index f2e207c..48b6e6b 100644
--- a/src/jalview/datamodel/ContactMatrix.java
+++ b/src/jalview/datamodel/ContactMatrix.java
@@ -1,7 +1,10 @@
 package jalview.datamodel;
 
+import java.awt.Color;
 import java.math.BigInteger;
 import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.HashMap;
 import java.util.List;
 import java.util.Spliterator;
 import java.util.StringTokenizer;
@@ -147,45 +150,43 @@ public abstract class ContactMatrix implements ContactMatrixI
   }
 
   @Override
-  public boolean hasReferenceSeq()
+  public String getAnnotLabel()
   {
-    // TODO Auto-generated method stub
-    return false;
+    return "Contact Matrix";
   }
 
   @Override
-  public SequenceI getReferenceSeq()
+  public String getAnnotDescr()
   {
-    // TODO Auto-generated method stub
-    return null;
+    return "Contact Matrix";
   }
-
+  GroupSet grps = new GroupSet();
   @Override
-  public String getAnnotLabel()
+  public GroupSetI getGroupSet()
   {
-    return "Contact Matrix";
+    return grps;
   }
-
   @Override
-  public String getAnnotDescr()
+  public void setGroupSet(GroupSet makeGroups)
   {
-    return "Contact Matrix";
+    grps = makeGroups;
   }
-
   public static String contactToFloatString(ContactMatrixI cm)
   {
     StringBuilder sb = new StringBuilder();
-    for (int c=0;c<cm.getWidth();c++)
+    for (int c = 0; c < cm.getWidth(); c++)
     {
-      ContactListI cl=cm.getContactList(c);
-      if (cl!=null) {
-      for (int h=0;h<=cl.getContactHeight();h++)
+      ContactListI cl = cm.getContactList(c);
+      if (cl != null)
       {
-        if (sb.length()>0) {
-          sb.append('\t');
+        for (int h = 0; h <= cl.getContactHeight(); h++)
+        {
+          if (sb.length() > 0)
+          {
+            sb.append('\t');
+          }
+          sb.append(cl.getContactAt(h));
         }
-        sb.append(cl.getContactAt(h));
-      }
       }
     }
     return sb.toString();
@@ -195,29 +196,27 @@ public abstract class ContactMatrix implements ContactMatrixI
           int rows)
   {
     float[][] vals = new float[cols][rows];
-    StringTokenizer tabsep = new StringTokenizer(values,""+'\t');
-    int c=0,r=0;
-    
+    StringTokenizer tabsep = new StringTokenizer(values, "" + '\t');
+    int c = 0, r = 0;
     while (tabsep.hasMoreTokens())
     {
       double elem = Double.valueOf(tabsep.nextToken());
-      vals[c][r++]=(float) elem;
-      if (r>=vals[c].length)
+      vals[c][r++] = (float) elem;
+      if (r >= vals[c].length)
       {
-        r=0;
+        r = 0;
         c++;
       }
-      if (c>=vals.length)
+      if (c >= vals.length)
       {
-        
         break;
       }
     }
     if (tabsep.hasMoreElements())
     {
-      Console.warn("Ignoring additional elements for Float string to contact matrix parsing.");
+      Console.warn(
+              "Ignoring additional elements for Float string to contact matrix parsing.");
     }
-      
     return vals;
   }
 }